期刊
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
卷 137, 期 8, 页码 3031-3040出版社
AMER CHEMICAL SOC
DOI: 10.1021/ja512605w
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资金
- National Institutes of Health [9P41GM104601]
- National Science Foundation [PHY0822613]
- Texas Advanced Computing Center via Extreme Science and Engineering Discovery Environment grant [NSF-MCA93S028]
- NSF [OCI-0725070]
- State of Illinois
- NSF Physics of Living Systems program [PHY-1026665]
- Direct For Mathematical & Physical Scien [1430124] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC) [1440026] Funding Source: National Science Foundation
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P41GM104601] Funding Source: NIH RePORTER
Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rhos six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general.
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